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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-08-01 12:01:11 | 3 | |||||
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NucleoFinder Resource Report Resource Website 1+ mentions |
NucleoFinder (RRID:SCR_000368) | NucleoFinder | software resource | A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes. | nucleusome, position, promoter, analysis, downstream, nucleotide, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23297036 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nucleofinder, OMICS_00510 | https://omictools.com/nucleofinder-tool, https://bio.tools/nucleofinder | SCR_000368 | 2026-08-01 12:01:15 | 1 | ||||||
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GraphPad Resource Report Resource Website 1000+ mentions |
GraphPad (RRID:SCR_000306) | commercial organization | A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs. | company, data, graph, scientific, statistical, analysis, curve, fitting |
is listed by: SoftCite is parent organization of: GraphPad Prism |
Restricted | nlx_156835 | SCR_000306 | 2026-08-01 12:01:14 | 1284 | |||||||||
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ARB project Resource Report Resource Website 10+ mentions |
ARB project (RRID:SCR_000515) | ARB | software resource | Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations. | rrna sequence, rrna, phylogeny, alignment, analysis, protein, gene |
is listed by: Debian is related to: SILVA is related to: SINA has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:14985472 | Free, Available for download, Freely available | OMICS_01515 | https://sources.debian.org/src/arb/ | SCR_000515 | The ARB project | 2026-08-01 12:01:23 | 28 | |||||
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ROSTLAB Resource Report Resource Website 1+ mentions |
ROSTLAB (RRID:SCR_000792) | group | A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. | protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical |
has parent organization: Columbia University; New York; USA is parent organization of: PredictNLS is parent organization of: SNPdbe |
NLM LM007329; NLM GM50291 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31417 | http://cubic.bioc.columbia.edu/services/disis | SCR_000792 | Rost Group | 2026-08-01 12:01:19 | 1 | ||||||
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MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-08-01 12:02:53 | 0 | |||||||
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Golden Helix Incorporated Resource Report Resource Website 100+ mentions |
Golden Helix Incorporated (RRID:SCR_012191) | Golden Helix | commercial organization | Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine. | resource, portal, analysis, software |
is listed by: ScienceExchange is parent organization of: Golden Helix GenomeBrowse is parent organization of: SNP and Variation Suite SNP Analysis is parent organization of: SNP and Variation Suite CNV Analysis is parent organization of: SNP and Variation Suite |
Available to external user | SciEx_10349 | http://www.goldenhelix.com/Services, http://www.scienceexchange.com/facilities/golden-helix-inc | SCR_012191 | Golden Helix Inc., GoldenHelix.com | 2026-08-01 12:04:36 | 138 | ||||||
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GenomeJack Resource Report Resource Website 10+ mentions |
GenomeJack (RRID:SCR_012026) | GenomeJack | software resource | A genome browser specialized in next-generation sequencing data. | next-generation sequencing, genome, browser, analysis | is listed by: OMICtools | Free, Public | OMICS_02143 | SCR_012026 | 2026-08-01 12:04:32 | 32 | ||||||||
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Leica Application Suite X Resource Report Resource Website 500+ mentions |
Leica Application Suite X (RRID:SCR_013673) | LAS X | resource | Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes. | confocal, image, analysis, leica, microscope, microbiology | has parent organization: Leica Microsystems | Commercially available | http://www.leica-microsystems.com/products/microscope-software/software-for-life-science-research/las-easy-and-efficient/ | SCR_013673 | Leica LAS, Leica LAS AF Image Acquisition Software, Leica Application Suite X, Leica Application Suite X (LAS X), Leica LAS X Life Science Microscope Software, Leica LAS X LS, LASX, Leica LAS X Life Science software, LAS X | 2026-08-01 12:05:02 | 526 | |||||||
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WinMDI Software Resource Report Resource Website 10+ mentions |
WinMDI Software (RRID:SCR_013745) | Software to analyze flow cytometry listmode data files. | flow cytometry, analysis | http://facs.scripps.edu/software.html | SCR_013745 | Windows Multiple Document Interface software, Windows Multiple Document Interface for Flow Cytometry | 2026-08-01 12:05:03 | 26 | |||||||||||
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TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software resource, software application | MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7 | disease target, drug discovery, drug, matlab, gene network, genetic interaction, gene, drug screening, mutation driver, therapeutic target, drug candidate, compound, mapping, analysis | has parent organization: Biomedical Simulations Resource | Cancer | NIBIB P41-EB001978 | PMID:22952662 | Free, Under the terms of a Release Agreement., Please cite | nlx_152573 | http://bmsr.usc.edu/Software/TARGET/TARGET.html | SCR_001392 | 2026-08-01 12:10:36 | 7 | ||||
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Primate Embryo Gene Expression Resource Resource Report Resource Website 1+ mentions |
Primate Embryo Gene Expression Resource (RRID:SCR_002765) | PREGER | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods. | primate, embryo, gene, expression, embryologist, microarray, rhesus, monkey, oocyte, embryo, cdna, library, molecular, analysis, stem cell, oocyte quality, preimplantation development, transcription |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Temple University School of Medicine; Pennsylvania; USA |
NIH Office of the Director R24 OD012221; NCRR RR15253 |
PMID:14724133 PMID:17147927 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24366 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | SCR_002765 | PREGER Online, Preger.org | 2026-08-01 12:10:42 | 6 | ||||
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AltAnalyze - Alternative Splicing Analysis Tool Resource Report Resource Website 50+ mentions |
AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) | AltAnalyze | software resource, software application | Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph. | analysis, alternative splicing, microarray, calculate, pathway, ontology, domain, microrna, targeting, splicing, microarry, rna-seq, metabolomics, mac osx, windows, ubuntu, cross platform, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Cytoscape has parent organization: University of California at San Francisco; California; USA |
PMID:20513647 | Free, Available for download, Freely available | nif-0000-30083, OMICS_02250, biotools:altanalyze | https://bio.tools/altanalyze | SCR_002951 | Alternative Splicing Analysis Tool | 2026-08-01 12:10:34 | 81 | |||||
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Nipype Resource Report Resource Website 500+ mentions |
Nipype (RRID:SCR_002502) | Nipype | software resource, software application | A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. | magnetic resonance, python, workflow, analysis, pipeline, interface, data processing, neuroimaging |
is used by: Forward: Accurate finite element electromagnetic head models is used by: fMRIPrep is used by: NHP BIDS is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
PMID:21897815 | Free, Available for download, Freely available | nlx_155901 | http://www.nitrc.org/projects/nipype | SCR_002502 | Nipype: Neuroimaging in Python Pipeline and Interfaces, NIPY Pipeline and Interfaces | 2026-08-01 12:10:40 | 822 | |||||
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Blast2GO Resource Report Resource Website 5000+ mentions |
Blast2GO (RRID:SCR_005828) | B2G | software resource, software application | An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, visualization, analysis, functional genomics, editor, statistical analysis, slimmer-type tool, ontology or annotation editor, functional analysis, direct acyclic graph, analysis, high throughput, functional genomics |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Principe Felipe Research Centre; Valencia; Spain |
MCyT GEN 2001 - 4885-C05-03; eTumour Project FP6-2002-LIFESCIHEALTH 503094 |
PMID:16081474 | Free for academic use | OMICS_01475, nlx_149335 | SCR_005828 | Blast2GO (B2G) | 2026-08-01 12:10:38 | 8422 | |||||
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Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators. | stem cell, facility, la jolla, pluripotent stem cells, ipsc, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014856 | SBP Medical Discovery Institute Stem Cell Core, SBP Stem Cell Core | 2026-08-01 12:11:04 | 0 | ||||||||||
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Interact Resource Report Resource Website 1+ mentions |
Interact (RRID:SCR_019254) | software resource | Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software. | Synchronized viewing, analysis, video footage, audio files, observational research, video coding | Restricted | SCR_019254 | 2026-08-01 12:06:24 | 5 | |||||||||||
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Thermo Fisher: GeneChip� Scanner 3000 7G Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk, https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-08-01 12:05:40 | 1 | |||||||||
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NZYTech Resource Report Resource Website 10+ mentions |
NZYTech (RRID:SCR_016772) | organization | Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins. | biomaterial, analysis, service, production, supplier, molecular, biology, diagnostics, enzyme, protein | grid.436825.e, Wikidata: Q30291029 | https://ror.org/00rtryt44 | SCR_016772 | Lda. � Genes and Enzymes, NZYTech | 2026-08-01 12:05:41 | 11 | |||||||||
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BioNano: Irys system Resource Report Resource Website 10+ mentions |
BioNano: Irys system (RRID:SCR_016754) | instrument resource | System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies. | instrument, Irys, system, BioNano Genomics, BioNanomatrix, optical, next, generation, mapping, sequence, assembly, structural, variation, analysis, data, | Commercially available | https://bionanogenomics.com/wp-content/uploads/2017/01/2016-Irys-System-Brochure.pdf | https://bionanogenomics.com/technology/genome-assembly/ | SCR_016754 | 2026-08-01 12:05:53 | 35 |
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